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  <section id="about">
<h1>About<a class="headerlink" href="#about" title="Link to this heading">¶</a></h1>
<section id="about-timsconvert">
<h2>About TIMSCONVERT<a class="headerlink" href="#about-timsconvert" title="Link to this heading">¶</a></h2>
<p>TIMSCONVERT is a workflow designed for mass spectrometrists that allows for the conversion of raw data from Bruker
timsTOF series mass spectrometers (i.e. Pro, fleX, SCP, HT, etc.) to open data formats (i.e. mzML and imzML) that:</p>
<ol class="arabic simple">
<li><p>are compatible with downstream open source data analysis platforms.</p></li>
<li><p>incorporate trapped ion mobility spectrometry (TIMS) data into these open formats.</p></li>
<li><p>does not require any programming experience.</p></li>
</ol>
</section>
<section id="timstof-file-formats">
<h2>timsTOF File Formats<a class="headerlink" href="#timstof-file-formats" title="Link to this heading">¶</a></h2>
<p>All Bruker data is housed in a directory with the .d extension. Within the directory, the acquisition software and type
of experiment conducted (i.e. acquisition mode) determines the data format. LC-MS(/MS) experiments acquired using
Bruker otofControl use the BAF file format, which is widely supported by both proprietary (i.e. Bruker DataAnalysis,
CompassXport) and open-source (i.e. Proteowizard MSConvert) data conversion/analysis software. The raw binary data is
housed in the <code class="docutils literal notranslate"><span class="pre">analysis.baf</span></code> file, while the metadata and recalibration information are stored in SQLite databases
titled <code class="docutils literal notranslate"><span class="pre">analysis.sqlite</span></code> and <code class="docutils literal notranslate"><span class="pre">calibration.sqlite</span></code>, respectively.</p>
<p>LC-MS(/MS) and MALDI-MS(/MS) dried droplet and mass spectrometry imaging experiments acquired using Bruker timsControl
use the TSF file format. Compared to BAF files, TSF files have the advantage of store data in a much more efficient
manner, but have more limited support from both proprietary and open-source software. Experiments designed to acquire
TIMS data (LC-TIMS-MS(/MS), MALDI-TIMS-MS(/MS) dried droplet and mass spectrometry imaging) use the TDF file formats,
which are similar to TSF files but also contain TIMS data. Run metadata are stored in the <code class="docutils literal notranslate"><span class="pre">analysis.tsf</span></code>/
<code class="docutils literal notranslate"><span class="pre">analysis.tdf</span></code> SQLite databases, raw binary data are stored in the <code class="docutils literal notranslate"><span class="pre">analysis.tsf_bin</span></code>/<code class="docutils literal notranslate"><span class="pre">analysis.tdf_bin</span></code> files,
and recalibration data are stored in the <code class="docutils literal notranslate"><span class="pre">calibration.sqlite</span></code> SQLite database.</p>
</section>
<section id="dimensionality-of-timstof-data">
<h2>Dimensionality of timsTOF Data<a class="headerlink" href="#dimensionality-of-timstof-data" title="Link to this heading">¶</a></h2>
<p>Example of dimensionality of LC-TIMS-MS/MS data and a simplified corresponding mzML schema. Elements in the simplified
mzML schema are color coded by the corresponding data in the chromatograms/mobilograms/spectra. At a given retention
time in the chromatogram (indicated in pink), an MS1 spectrum may be visualized in the form of a three dimensional plot
generated from <em>m/z</em>, intensity, and ion mobility arrays (indicated in orange). Precursor ions of interest found in MS1
spectra (indicated in purple) can be further analyzed by plotting <em>m/z</em> and intensity arrays for MS/MS spectra
(indicated in teal). These spectral identifiers (i.e. retention time, precursor <em>m/z</em>, precursor 1/K0) may be used to
locate the corresponding MS/MS spectrum from Bruker DataAnalysis or other data visualization software of choice.</p>
<img alt="Figure showing how different dimensions of timsTOF data are represented in converted open data formats." src="_images/dimensions.png" />
</section>
<section id="example-acquisition-modes-for-file-conversion">
<h2>Example Acquisition Modes for File Conversion<a class="headerlink" href="#example-acquisition-modes-for-file-conversion" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p>LC-MS(/MS) (BAF or TSF) -&gt; mzML</p></li>
<li><p>LC-TIMS-MS(/MS) (TDF) -&gt; mzML</p></li>
<li><p>MALDI-MS(/MS) Dried Droplet (TSF) -&gt; mzML</p></li>
<li><p>MALDI-MS Imaging Mass Spectrometry (TSF) -&gt; imzML</p></li>
<li><p>MALDI-TIMS-MS(/MS) Dried Droplet (TDF) -&gt; mzML</p></li>
<li><p>MALDI-TIMS-MS Imaging Mass Spectrometry (TDF) -&gt; imzML</p></li>
</ul>
</section>
<section id="downstream-data-analysis">
<h2>Downstream Data Analysis<a class="headerlink" href="#downstream-data-analysis" title="Link to this heading">¶</a></h2>
<p>Examples of downstream data analysis platforms include and are not limited to:
* <a class="reference external" href="https://gnps.ucsd.edu/">Global Natural Products Social (GNPS)</a>
* <a class="reference external" href="https://cardinalmsi.org/">Cardinal MSI</a>
* <a class="reference external" href="https://chasemc.github.io/IDBac/">IDBac</a>
* <a class="reference external" href="http://mzmine.github.io/">MZmine</a></p>
</section>
</section>


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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#about-timsconvert">About TIMSCONVERT</a></li>
<li class="toctree-l2"><a class="reference internal" href="#timstof-file-formats">timsTOF File Formats</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dimensionality-of-timstof-data">Dimensionality of timsTOF Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="#example-acquisition-modes-for-file-conversion">Example Acquisition Modes for File Conversion</a></li>
<li class="toctree-l2"><a class="reference internal" href="#downstream-data-analysis">Downstream Data Analysis</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="local.html">GUI Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="local.html#command-line-usage">Command Line Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="timsconvert.html">TIMSCONVERT Source Code</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Modules</a></li>
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